cran: Mercator | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0183417

Association of gene expression with biomass content and composition in sugarcane
Cited by: 23
Author(s): Nam V. Hoang, Agnelo Furtado, Angela O'Keeffe, Frederik C. Botha, Robert J. Henry
Software Mentions: 15
Published: over 7 years ago

10.1111/eva.13202

Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation
Cited by: 15
Author(s): Felix Vaux, Sandra Bohn, John R. Hyde, Kathleen G. O’Malley
Software Mentions: 15
Published: almost 4 years ago

10.3390/ijms21218148

Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.
Cited by: 25
Author(s): Stephanie Schaarschmidt, Axel Fischer, Lovely Mae F Lawas, Rejbana Alam, Endang M. Septiningsih, Julia Bailey‐Serres, Krishna Jagadish, Bruno Huettel, Dirk K. Hincha, Ellen Zuther
Software Mentions: 11
Published: about 4 years ago

10.3390/cells9030779

Transcriptomic Insights into Mechanisms of Early Seed Maturation in the Garden Pea (Pisum sativum L.)
Cited by: 12
Author(s): Yury V. Malovichko, O. Y. Shtark, Ekaterina N. Vasileva, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 10
Published: over 4 years ago

10.1038/s42003-018-0171-y

Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species
Cited by: 33
Author(s): Stefan Reuscher, Tomohisa Furuta, Kanako Bessho‐Uehara, Michele Cosi, Kshirod K. Jena, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Motoyuki Ashikari
Software Mentions: 9
Published: about 6 years ago

10.1371/journal.pbio.1000343

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species
Cited by: 190
Author(s): Robert K. Bradley, Xiaoyong Li, Cole Trapnell, Stuart M. Davidson, Lior Pachter, Hou Cheng Chu, Leath A. Tonkin, Mark D. Biggin, Michael B. Eisen
Software Mentions: 8
Published: over 14 years ago

10.3389/fgene.2019.00654

The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome
Cited by: 5
Author(s): Nam V. Hoang, Agnelo Furtado, Virginie Perlo, Frederik C. Botha, Robert J. Henry
Software Mentions: 8
Published: over 5 years ago

10.3389/fpls.2021.693039

Far-Red Light-Induced Azolla filiculoides Symbiosis Sexual Reproduction: Responsive Transcripts of Symbiont Nostoc azollae Encode Transporters Whilst Those of the Fern Relate to the Angiosperm Floral Transition
Cited by: 5
Author(s): Laura W. Dijkhuizen, Badraldin Ebrahim Sayed Tabatabaei, Paul Brouwer, Niels Rijken, Valerie A. Buijs, Erbil Güngör, Henriette Schluepmann
Software Mentions: 7
Published: over 3 years ago

10.1186/s12870-020-02808-3

Integrated Transcriptomic and Metabolomic analysis reveals a transcriptional regulation network for the biosynthesis of carotenoids and flavonoids in ‘Cara cara’ navel Orange
Cited by: 18
Author(s): Haipeng Zhang, Jiajing Chen, Zhaoxin Peng, Meiyan Shi, Xiao Liu, Wen Huang, Youwu Jiang, Yunjiang Cheng, Juan Xu, Hongyan Zhang
Software Mentions: 7
Published: almost 4 years ago

10.1186/1471-2105-10-S14-S6

Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life
Cited by: 30
Author(s): Vincent Smith, Simon Rycroft, Kehan Harman, Ben Scott, David Roberts
Software Mentions: 6
Published: about 15 years ago

10.1371/journal.pone.0137340

Dispersal and Diving Adjustments of the Green Turtle Chelonia mydas in Response to Dynamic Environmental Conditions during Post-Nesting Migration
Cited by: 21
Author(s): Philippine Chambault, David Pinaud, Vincent Vantrepotte, Laurent Kelle, Mathieu Entraygues, Christophe Guinet, Rachel Berzins, Karin Bilo, Philippe Gaspar, Benoı̂t de Thoisy, Yvon Le Maho, Damien Chevallier
Software Mentions: 6
Published: about 9 years ago

10.1186/s12284-016-0098-1

Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress
Cited by: 32
Author(s): Elena Baldoni, Paolo Bagnaresi, Franca Locatelli, Monica Mattana, Annamaria Genga
Software Mentions: 6
Published: over 8 years ago

10.3390/genes11040428

LSTrAP-Cloud: A User-Friendly Cloud Computing Pipeline to Infer Coexpression Networks
Cited by: 9
Author(s): Qiao Wen Tan, Wooi-Boon Goh, Marek Mutwil
Software Mentions: 6
Published: over 4 years ago

10.1186/s12864-020-06795-5

Transcriptomic and biochemical investigations support the role of rootstock-scion interaction in grapevine berry quality
Cited by: 27
Author(s): Alessandra Zombardo, Cristina Crosatti, Paolo Bagnaresi, Laura Bassolino, Noam Reshef, Sergio Puccioni, Primetta Faccioli, Alessio Tafuri, Massimo Delledonne, Aaron Fait, Paolo Storchi, Luigi Cattivelli, Erica Mica
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-019-6444-0

The transcriptome of Pinus pinaster under Fusarium circinatum challenge
Cited by: 18
Author(s): Laura Hernandez‐Escribano, Erik A. Visser, Eugenia Iturritxa, Rosa Raposo, Sanushka Naidoo
Software Mentions: 5
Published: almost 5 years ago

10.3389/fpls.2021.715683

Morphological, Physiological, and Molecular Responses of Sweetly Fragrant Luculia gratissima During the Floral Transition Stage Induced by Short-Day Photoperiod
Cited by: 0
Author(s): Xiongfang Liu, Yat-wah Wan, Jing An, Xiujiao Zhang, Yurong Cao, Zhenghong Li, Xiuxian Liu, Hong Ma
Software Mentions: 5
Published: over 3 years ago

10.3390/plants9091176

Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling
Cited by: 19
Author(s): Ivan Tsers, Vladimir Gorshkov, Natalia Gogoleva, Olga Parfirova, Olga Petrova, Alexander A. Kamnev
Software Mentions: 5
Published: over 4 years ago

10.1093/jxb/erz546

Transcriptional and biochemical analyses of gibberellin expression and content in germinated barley grain
Cited by: 16
Author(s): Natalie S. Betts, Christoph Dockter, Oliver Berkowitz, Helen Collins, Michelle Hooi, Qiongxian Lu, Rachel A. Burton, Vincent Bulone, Birgitte Skadhauge, James Whelan, Geoffrey B. Fincher
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2021.661296

Combined Analysis of Volatile Terpenoid Metabolism and Transcriptome Reveals Transcription Factors Related to Terpene Synthase in Two Cultivars of Dendrobium officinale Flowers
Cited by: 20
Author(s): Ninghong Li, Yan Dong, Min Lv, Qian Li, Xinwei Sun, Liu Lin, Yongping Cai, Honghong Fan
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2021.645443

Global Transcriptome and Weighted Gene Co-expression Network Analyses of Growth-Stage-Specific Drought Stress Responses in Maize
Cited by: 21
Author(s): Songtao Liu, Tinashe Zenda, Anyi Dong, Yatong Yang, Nan Wang, Huijun Duan
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-015-1816-6

Uncovering co-expression gene network modules regulating fruit acidity in diverse apples
Cited by: 54
Author(s): Yang Bai, Laura Dougherty, Lailiang Cheng, Gan-Yuan Zhong, Kenong Xu
Software Mentions: 4
Published: over 9 years ago

10.1093/jxb/erx224

Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype
Cited by: 38
Author(s): Noé Cochetel, Frédéric Escudié, Sarah Jane Cookson, Zhanwu Dai, Philippe Vivin, Pierre‐François Bert, Mindy Muñoz, Serge Delrot, Christophe Klopp, Nathalie Ollat, Virginie Lauvergeat
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-021-90607-7

Defining the combined stress response in wild Arachis
Cited by: 12
Author(s): Ana Paula Zotta Mota, Ana Cristina Miranda Brasileiro, Bruna Vidigal, Thais Nicolini Oliveira, Andressa da Cunha Quintana Martins, Mario Alfredo de Passos Saraiva, Ana Cláudia Guerra Araújo, Roberto Coiti Togawa, Maria Fátima Grossi-de-Sá, P. M. Guimarães
Software Mentions: 4
Published: over 3 years ago

10.1093/database/bav096

Ensembl comparative genomics resources
Cited by: 315
Author(s): Javier Herrero, Matthieu Muffato, Kathryn Beal, Stephen Fitzgerald, Leo I. Gordon, Miguel Pignatelli, Albert J. Vilella, Stephen M. J. Searle, M Ridwan Amode, Simon Brent, William Spooner, Eugene Kulesha, Andy Yates, Paul Flicek
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-015-2108-x

Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos
Cited by: 18
Author(s): Delasa Aghamirzaie, Dhruv Batra, Lenwood S. Heath, Andrew M. Schneider, Ruth Grene, Eva Collakova
Software Mentions: 4
Published: about 9 years ago

10.1002/ece3.1838

Squares of different sizes: effect of geographical projection on model parameter estimates in species distribution modeling
Cited by: 14
Author(s): Lara Budic, Gregor Didenko, Carsten F. Dormann
Software Mentions: 4
Published: about 9 years ago

10.1093/aobpla/ply013

Patterns of alternative splicing vary between species during heat stress
Cited by: 25
Author(s): Sumetha Kannan, Gillian Halter, Tanya Renner, Elizabeth R. Waters
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms22147266

Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts
Cited by: 12
Author(s): Weitao Li, Li Huang, Nian Liu, Manish K. Pandey, Yuning Chen, Cheng Ling, Jianbin Guo, Bin Yu, Huaiyong Luo, Xiaojing Zhou, Dongxin Huai, Weigang Chen, Liying Yan, Xin Wang, Yong Lei, Rajeev K. Varshney, Boshou Liao, Huifang Jiang
Software Mentions: 4
Published: over 3 years ago

10.1038/s41438-021-00566-3

Sex-biased genes and metabolites explain morphologically sexual dimorphism and reproductive costs in Salix paraplesia catkins
Cited by: 8
Author(s): Zeyu Cai, Congcong Yang, Jianchun Liao, Haifeng Song, Sheng Zhang
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pbio.1002512

Spatial Embedding and Wiring Cost Constrain the Functional Layout of the Cortical Network of Rodents and Primates
Cited by: 160
Author(s): Szabolcs Horvát, Răzvan Gămănuţ, Mária Ercsey-Ravasz, Loïc Magrou, Bianca Gămănuț, David C. Van Essen, Andreas Burkhalter, Kenneth Knoblauch, Zoltán Toroczkai, Henry Kennedy
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pgen.1009229

3D genome evolution and reorganization in the Drosophila melanogaster species group
Cited by: 24
Author(s): Nicole S. Torosin, Aparna Anand, Tirupathi Rao Golla, Weihuan Cao, Chris Ellison
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0253741

Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato)
Cited by: 0
Author(s): Mihai-Silviu Tomescu, Selisha A. Sooklal, Thuto Ntsowe, Previn Naicker, Barbara Darnhofer, Robert H. Archer, Stoyan Stoychev, Dirk Swanevelder, Ruth Birner‐Grünberger, Karl Rumbold
Software Mentions: 4
Published: over 3 years ago

10.3390/microorganisms7090315

Dual RNA-Seq Analysis of the Pine-Fusarium circinatum Interaction in Resistant (Pinus tecunumanii) and Susceptible (Pinus patula) Hosts
Cited by: 17
Author(s): Erik A. Visser, Jill L. Wegrzyn, Emma Theodora Steenkamp, Alexander Andrew Myburg, Sanushka Naidoo
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0120014

Poor Transferability of Species Distribution Models for a Pelagic Predator, the Grey Petrel, Indicates Contrasting Habitat Preferences across Ocean Basins
Cited by: 80
Author(s): Leigh G. Torres, Philip Sutton, David R. Thompson, Karine Delord, Henri Weimerskirch, Paul M. Sagar, Erica Sommer, Ben J. Dilley, Peter G. Ryan, Richard A. Phillips
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pgen.1006464

Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages
Cited by: 52
Author(s): Lauren Gibilisco, Qi Zhou, Shivani Mahajan, Doris Bachtrog
Software Mentions: 4
Published: about 8 years ago

10.1074/mcp.M115.049205

Drought and Recovery: Independently Regulated Processes Highlighting the Importance of Protein Turnover Dynamics and Translational Regulation in Medicago truncatula
Cited by: 37
Author(s): David Lyon, María Ángeles Castillejo, Vlora Mehmeti-Tershani, Christiana Staudinger, Christoph Kleemaier, Stefanie Wienkoop
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-020-07091-y

Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning
Cited by: 10
Author(s): Fernando Henrique Correr, Guilherme Kenichi Hosaka, Fernando Barreto, Isabella Barros Valadão, Thiago Willian Almeida Balsalobre, Agnelo Furtado, Robert J. Henry, Monalisa Sampaio Carneiro, Gabriel Rodrigues Alves Margarido
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0092148

Phylogeography of the Tropical Planktonic Foraminifera Lineage Globigerinella Reveals Isolation Inconsistent with Passive Dispersal by Ocean Currents
Cited by: 40
Author(s): Agnes Weiner, Manuel F. G. Weinkauf, Atsushi Kurasawa, Kate Darling, Michal Kučera, Guido W. Grimm
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pgen.1003748

Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression
Cited by: 91
Author(s): Mathilde Paris, Tommy Kaplan, Xiao Yong Li, Jacqueline E. Villalta, Susan E. Lott, Michael B. Eisen
Software Mentions: 4
Published: over 11 years ago

10.3389/fpls.2019.01249

Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence
Cited by: 9
Author(s): Anna Furches, David Kainer, Deborah Weighill, Annabel Large, Piet Jones, Angelica M. Walker, Jonathon Romero, João Gabriel Felipe Machado Gazolla, Wayne Joubert, Manesh Shah, Jared Streich, Priya Ranjan, Jeremy Schmutz, Avinash Sreedasyam, David Macaya‐Sanz, Nan Zhao, Madhavi Z. Martin, Xiaolan Rao, Richard A. Dixon, Stephen P. DiFazio, Timothy J. Tschaplinski, Jay Chen, Gerald A. Tuskan, Daniel Jacobson
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0143412

Transcriptome Analysis of Plant Hormone-Related Tomato (Solanum lycopersicum) Genes in a Sunlight-Type Plant Factory
Cited by: 10
Author(s): Yusuke Tanigaki, Takanobu Higashi, Kotaro Takayama, Atsushi J. Nagano, Mie N. Honjo, Hirokazu Fukuda
Software Mentions: 4
Published: about 9 years ago

10.1111/tpj.14179

Computational aspects underlying genome to phenome analysis in plants
Cited by: 47
Author(s): Anthony Bolger, Hendrik Poorter, Kathryn Dumschott, Marie E. Bolger, Daniel Arend, Sonia Osorio, Heidrun Gundlach, Klaus Mayer, Matthias Lange, Uwe Scholz, Björn Usadel
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpls.2021.653183

Transcriptome Analysis of Tetraploid and Octoploid Common Reed (Phragmites australis)
Cited by: 5
Author(s): Cui Wang, Tong Wang, Meiqi Yin, Franziska Eller, Lele Liu, Hans Brix, Weihua Guo
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0198191

Early responses to dehydration in contrasting wild Arachis species
Cited by: 21
Author(s): C. C. Vinson, Ana Paula Zotta Mota, Thais Nicolini Oliveira, Larissa Arrais Guimarães, Soraya C. M. Leal‐Bertioli, Thomas Christopher Rhys Williams, Alexandre Lima Nepomuceno, Mario Alfredo Passos Saraiva, Ana Cláudia Guerra Araújo, P. M. Guimarães, Ana Cristina Miranda Brasileiro
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2019.01605

De Novo Transcriptome Analysis of Durum Wheat Flag Leaves Provides New Insights Into the Regulatory Response to Elevated CO2 and High Temperature
Cited by: 26
Author(s): Rubén Vicente, Anthony Bolger, Rafael Martínez‐Carrasco, Pilar Pérez Pérez, Elena Gutiérrez, Björn Usadel, Rosa Morcuende
Software Mentions: 4
Published: about 5 years ago

10.1093/jxb/eru094

Identification of predominant genes involved in regulation and execution of senescence-associated nitrogen remobilization in flag leaves of field grown barley
Cited by: 63
Author(s): Julien Hollmann, Per L. Gregersen, Karin Krupinska
Software Mentions: 4
Published: over 10 years ago

10.3389/fpls.2015.00967

The effector repertoire of Fusarium oxysporum determines the tomato xylem proteome composition following infection
Cited by: 55
Author(s): Fleur Gawehns, Lisong Ma, Oskar Bruning, Petra M. Houterman, Sjef Boeren, Ben J. C. Cornelissen, Martijn Rep, Frank L. W. Takken
Software Mentions: 4
Published: about 9 years ago

10.3390/plants8120531

Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship between Photosynthesis and Leaf Development
Cited by: 9
Author(s): Giulio Testone, Elena Baldoni, Maria Adelaide Iannelli, Chiara Nicolodi, Elisabetta Di Giacomo, Fabrizio Pietrini, Giovanni Mele, Donato Giannino, Giovanna Frugis
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-5908-6

Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties
Cited by: 17
Author(s): Nadia Bertazzon, Paolo Bagnaresi, Vally Forte, Elisabetta Mazzucotelli, Luisa Filippin, Davide Guerra, Antonella Zechini, Luigi Cattivelli, Elisa Angelini
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-67833-6

miRNAs involved in transcriptome remodeling during pollen development and heat stress response in Solanum lycopersicum
Cited by: 19
Author(s): Mario Keller, Enrico Schleiff, Stefan Simm
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pcbi.1000392

Fast Statistical Alignment
Cited by: 303
Author(s): Robert K. Bradley, Anjeanette Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian Holmes, Lior Pachter
Software Mentions: 4
Published: over 15 years ago

10.1186/1471-2229-14-185

Genome-wide analysis reveals divergent patterns of gene expression during zygotic and somatic embryo maturation of Theobroma cacaoL., the chocolate tree
Cited by: 25
Author(s): Siela N. Maximova, Sergio Florez, Xiangling Shen, Nicolas Niemenak, Yufan Zhang, Wayne R. Curtis, Mark J. Guiltinan
Software Mentions: 3
Published: over 10 years ago

10.3390/ijms22105087

Genome-Wide Identification of Barley Long Noncoding RNAs and Analysis of Their Regulatory Interactions during Shoot and Grain Development
Cited by: 2
Author(s): Sebastian Gasparis, Mateusz Przyborowski, Anna Nadolska‐Orczyk
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms21197404

Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana
Cited by: 5
Author(s): Yanqiao Zhu, Oliver Berkowitz, Jennifer Selinski, Andreas Hartmann, Reena Narsai, Yan Wang, Peisheng Mao, James Whelan
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2105-12-144

Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization
Cited by: 5
Author(s): Krishna M. Roskin, Benedict Paten, David Haussler
Software Mentions: 3
Published: over 13 years ago

10.3390/ijms21207603

Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (Glycine max) Tissues during Early Seed Development
Cited by: 8
Author(s): Shuo Sun, Changyu Yi, Jing Ma, Shoudong Wang, Marta Peirats‐Llobet, Mathew G. Lewsey, James Whelan, Huixia Shou
Software Mentions: 3
Published: about 4 years ago

10.1186/s12859-021-03992-1

Pattern recognition in lymphoid malignancies using CytoGPS and Mercator
Cited by: 2
Author(s): Zachary B. Abrams, Dwayne G. Tally, Lin Zhang, Caitlin E. Coombes, Philip R. O. Payne, Lynne V. Abruzzo
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12870-020-2260-6

Transcriptomic study of pedicels from GA3-treated table grape genotypes with different susceptibility to berry drop reveals responses elicited in cell wall yield, primary growth and phenylpropanoids synthesis
Cited by: 6
Author(s): Marco Meneses, Miguel García-Rojas, Claudia Muñoz-Espinoza, Tomás Carrasco-Valenzuela, Bruno G. Defilippi, Mauricio González-Agüero, Claudio Meneses, Rodrigo Infante, Patricio Hinrichsen
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2229-13-220

Differential transcriptome analysis of glandular and filamentous trichomes in Artemisia annua
Cited by: 83
Author(s): Sandra Soetaert, Christophe Van Neste, Mado Vandewoestyne, Steven R. Head, Alain Goossens, Filip Van Nieuwerburgh, Dieter Deforce
Software Mentions: 3
Published: about 11 years ago

10.1186/s12870-018-1373-7

Comparative root transcriptome of wild Arachis reveals NBS-LRR genes related to nematode resistance
Cited by: 24
Author(s): Ana Paula Zotta Mota, Bruna Vidigal, Étienne Danchin, Roberto Coiti Togawa, Soraya C. M. Leal‐Bertioli, David J. Bertioli, Ana Cláudia Guerra Araújo, Ana Cristina Miranda Brasileiro, P. M. Guimarães
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms151120833

Genome-Wide Transcriptome Profiles of Rice Hybrids and Their Parents
Cited by: 11
Author(s): E Zhiguo, Shanshan Huang, Yuping Zhang, Ge Liu, Lei Wang
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-018-22798-5

Transcriptomic analysis of transgressive segregants revealed the central role of photosynthetic capacity and efficiency in biomass accumulation in sugarcane
Cited by: 14
Author(s): Ratnesh Singh, Tyler Jones, Ching Man Wai, John Jifon, Chifumi Nagai, Ray Ming, Qingyi Yu
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-021-84461-w

Transcriptional profiling of two contrasting genotypes uncovers molecular mechanisms underlying salt tolerance in alfalfa
Cited by: 11
Author(s): Rakesh Kaundal, Naveen Duhan, Bibhudendra Acharya, Manju V. Pudussery, Jorge Ferreira, Donald L. Suarez, Devinder Sandhu
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pbio.3000094

Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila
Cited by: 26
Author(s): Chris Ellison, Doris Bachtrog
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-016-3083-6

De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia
Cited by: 30
Author(s): Marina Mora-Ortiz, Martin Swain, Martin Vickers, Matthew J. Hegarty, Rhys Kelly, Lydia Smith, Leif Skøt
Software Mentions: 3
Published: about 8 years ago

10.3390/ijms21114070

Transcriptome-Based Analysis of Tomato Genotypes Resistant to Bacterial Spot (Xanthomonas perforans) Race T4
Cited by: 7
Author(s): Rui Shi, Dilip R. Panthee
Software Mentions: 3
Published: over 4 years ago

10.1093/jxb/erz524

Integrative analysis of the nuclear proteome in Pinus radiata reveals thermopriming coupled to epigenetic regulation
Cited by: 27
Author(s): Laura Lamelas, Luís Valledor, Mónica Escandón, Glória Pinto, María Jesús Cañal, Monica Meijón
Software Mentions: 3
Published: about 5 years ago

10.1002/pld3.56

Waterlogging affects plant morphology and the expression of key genes in tef ( Eragrostis tef )
Cited by: 21
Author(s): Gina Cannarozzi, Annett Weichert, Mirjam Schnell, Celia Ruiz, Svenja Bossard, Regula Blösch, Sonia Plaza-Wüthrich, Solomon Chanyalew, Kebebew Assefa, Zerihun Tadele
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2018.01248

Microscopic and Proteomic Analysis of Dissected Developing Barley Endosperm Layers Reveals the Starchy Endosperm as Prominent Storage Tissue for ER-Derived Hordeins Alongside the Accumulation of Barley Protein Disulfide Isomerase (HvPDIL1-1)
Cited by: 13
Author(s): Valentin Roustan, Pierre-Jean Roustan, Marieluise Weidinger, Siegfried Reipert, Eszter Kapusi, Azita Shabrangy, Eva Stöger, Wolfram Weckwerth, Verena Ibl
Software Mentions: 3
Published: over 6 years ago

10.1534/g3.119.400023

Adenine Methylation in Drosophila Is Associated with the Tissue-Specific Expression of Developmental and Regulatory Genes
Cited by: 19
Author(s): Kinnary Shah, Weihuan Cao, Chris Ellison
Software Mentions: 3
Published: over 5 years ago

10.1111/j.1467-7652.2011.00625.x

Large‐scale transcriptome analysis in chickpea ( Cicer arietinum L.), an orphan legume crop of the semi‐arid tropics of Asia and Africa
Cited by: 239
Author(s): Pavana J Hiremath, Andrew Farmer, Steven B. Cannon, Jimmy E. Woodward, Himabindu Kudapa, Reetu Tuteja, Ashish Kumar, BhanuPrakash Amindala, Benjamin Mulaosmanovic, Neha Gujaria, L. Krishnamurthy, Pooran M. Gaur, Polavarapu B. KaviKishor, Trushar Shah, R. Srinivasan, Marc Lohse, Yongli Xiao, Christopher D. Town, Douglas R. Cook, Gregory D. May, Rajeev K. Varshney
Software Mentions: 3
Published: over 13 years ago

10.1186/1471-2164-14-340

Insights into organ-specific pathogen defense responses in plants: RNA-seq analysis of potato tuber-Phytophthora infestans interactions
Cited by: 98
Author(s): Liangliang Gao, Zheng Jin Tu, Benjamin P. Millett, James M. Bradeen
Software Mentions: 3
Published: over 11 years ago

10.3389/fpls.2019.00823

Transcriptional Insight Into Brassica napus Resistance Genes LepR3 and Rlm2-Mediated Defense Response Against the Leptosphaeria maculans Infection
Cited by: 13
Author(s): Tengsheng Zhou, Wen Xu, Arvind H. Hirani, Zheng Liu, Phạm Anh Tuấn, Belay T. Ayele, Fouad Daayf, P. B. E. McVetty, Robert Duncan, Genyi Li
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0151105

Transcriptome Profiling of Two Asparagus Bean (Vigna unguiculata subsp. sesquipedalis) Cultivars Differing in Chilling Tolerance under Cold Stress
Cited by: 23
Author(s): Haidong Tan, Haitao Huang, Manman Tie, Yi Tang, Yunsong Lai, Huanxiu Li
Software Mentions: 3
Published: almost 9 years ago

10.3389/fpls.2015.01246

A De novo Transcriptomic Approach to Identify Flavonoids and Anthocyanins “Switch-Off” in Olive (Olea europaea L.) Drupes at Different Stages of Maturation
Cited by: 30
Author(s): Domenico Iaria, Adriana Chiappetta, Innocenzo Muzzalupo
Software Mentions: 3
Published: almost 9 years ago

10.3389/fpls.2021.673072

Genome-Wide Association Studies of Seed Performance Traits in Response to Heat Stress in Medicago truncatula Uncover MIEL1 as a Regulator of Seed Germination Plasticity
Cited by: 4
Author(s): Zhijuan Chen, Joseph Ly Vu, Benoît Ly Vu, Julia Buitink, Olivier Leprince, Jérôme Verdier
Software Mentions: 3
Published: over 3 years ago

10.1038/srep33151

De novo Transcriptome Analysis Reveals Distinct Defense Mechanisms by Young and Mature Leaves of Hevea brasiliensis (Para Rubber Tree)
Cited by: 37
Author(s): Yuxiao Fang, Hailiang Mei, Binhui Zhou, Xiaohu Xiao, Meng Yang, Yacheng Huang, Xiangyu Long, Songnian Hu, Chaorong Tang
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-015-2318-2

Transcriptome profiling of soybean (Glycine max) roots challenged with pathogenic and non-pathogenic isolates of Fusarium oxysporum
Cited by: 56
Author(s): Alessandra Lanubile, Usha Muppirala, Andrew J. Severin, Adriano Marocco, Gary P. Munkvold
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0231574

Genetic diversity and connectivity of Flaccisagitta enflata (Chaetognatha: Sagittidae) in the tropical Atlantic ocean (northeastern Brazil)
Cited by: 6
Author(s): Danielle C M Melo, Simone Maria de Albuquerque Lira, Ana Paula B. Moreira, Lucas Freitas, Camilla A D Lima, Fabiano L. Thompson, Arnaud Bertrand, Alex C. Silva, Sigrid Neumann‐Leitão
Software Mentions: 3
Published: over 4 years ago

10.3389/fpls.2017.01961

Rhizobium Impacts on Seed Productivity, Quality, and Protection of Pisum sativum upon Disease Stress Caused by Didymella pinodes: Phenotypic, Proteomic, and Metabolomic Traits
Cited by: 37
Author(s): Nima Ranjbar Sistani, Hans‐Peter Kaul, Getinet Desalegn, Stefanie Wienkoop
Software Mentions: 3
Published: about 7 years ago

10.1186/s12936-021-03668-4

Cross-border malaria in Northern Brazil
Cited by: 24
Author(s): Nicholas J. Arisco, Cassio Peterka, Márcia C. Castro
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1005395

Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma
Cited by: 35
Author(s): Sarah A. Gilmore, Mark Voorhies, Dana Gebhart, Anita Sil
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2017.01260

Tissue-Specific Floral Transcriptome Analysis of the Sexually Deceptive Orchid Chiloglottis trapeziformis Provides Insights into the Biosynthesis and Regulation of Its Unique UV-B Dependent Floral Volatile, Chiloglottone 1
Cited by: 16
Author(s): D. Wong, Ranamalie Amarasinghe, Claudia Rodriguez‐Delgado, Rodney Eyles, Eran Pichersky, Rod Peakall
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-021-07837-2

Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires
Cited by: 5
Author(s): Malin Elfstrand, Jun Chen, Michelle Cleary, Sandra Halecker, Katarina Ihrmark, Magnus Karlsson, Kateryna Davydenko, Jan Stenlid, Marc Stadler, Mikael Brandström Durling
Software Mentions: 3
Published: over 3 years ago

10.1186/s13068-014-0171-1

System-level network analysis of nitrogen starvation and recovery in Chlamydomonas reinhardtii reveals potential new targets for increased lipid accumulation
Cited by: 83
Author(s): Luís Valledor, Takeshi Furuhashi, Luis Recuenco-Muñoz, Stefanie Wienkoop, Wolfram Weckwerth
Software Mentions: 3
Published: about 10 years ago

10.1007/s11816-013-0282-3

Genomics and bioinformatics resources for translational science in Rosaceae
Cited by: 20
Author(s): Sook Jung, Dorrie Main
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pcbi.1009162

Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19
Cited by: 18
Author(s): Hamish Gibbs, Emily Nightingale, Yang Liu, James Cheshire, León Danon, Liam Smeeth, Carl A. B. Pearson, Chris Grundy, Adam J. Kucharski, Rosalind M Eggo
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-015-1633-y

De novo transcriptome characterization and gene expression profiling of the desiccation tolerant moss Bryum argenteum following rehydration
Cited by: 51
Author(s): Bei Gao, Daoyuan Zhang, Xiaoshuang Li, Yang Hong-yuan, Yuanming Zhang, Andrew J. Wood
Software Mentions: 3
Published: over 9 years ago

10.1016/j.dib.2020.106671

Dataset for transcriptome and physiological response of mature tomato seed tissues to light and heat during fruit ripening
Cited by: 1
Author(s): Elise Bizouerne, Benoît Ly Vu, Joseph Ly Vu, Jérôme Verdier, Julia Buitink, Olivier Leprince
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-018-4967-4

Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl
Cited by: 30
Author(s): V. Michelotti, Antonella Lamontanara, Giampaolo Buriani, Luigi Orrù, Antonio Cellini, Irene Donati, J. L. Vanneste, Luigi Cattivelli, G. Tacconi, Francesco Spinelli
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-019-1902-z

Transcriptomic response in symptomless roots of clubroot infected kohlrabi (Brassica oleracea var. gongylodes) mirrors resistant plants
Cited by: 29
Author(s): Stefan Ciaghi, Arne Schwelm, Sigrid Neuhauser
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1006108

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles
Cited by: 148
Author(s): Raúl Castanera, Leticia López-Varas, Alessandra Borgognone, Kurt LaButti, Alla Lapidus, Jeremy Schmutz, Jane Grimwood, Gúmer Pérez, Antonio G. Pisabarro, Igor V. Grigoriev, Jason E. Stajich, Lucı́a Ramı́rez
Software Mentions: 3
Published: over 8 years ago

10.3389/fpls.2021.641325

Genes That Mediate Starch Metabolism in Developing and Germinated Barley Grain
Cited by: 10
Author(s): Helen Collins, Natalie S. Betts, Christoph Dockter, Oliver Berkowitz, Ilka Braumann, José A. Cuesta-Seijo, Birgitte Skadhauge, James Whelan, Vincent Bulone, Geoffrey B. Fincher
Software Mentions: 3
Published: almost 4 years ago

10.3389/fpls.2021.722802

Effect and Response of Quercus ilex subsp. ballota [Desf.] Samp. Seedlings From Three Contrasting Andalusian Populations to Individual and Combined Phytophthora cinnamomi and Drought Stresses
Cited by: 18
Author(s): Bonoso San-Eufrasio, María Ángeles Castillejo, Mónica Labella-Ortega, Francisco J. Ruíz-Gómez, Rafael M. Navarro-Cerrillo, Marta Tienda-Parrilla, Jesús V. Jorrín‐Novo, María‐Dolores Rey
Software Mentions: 3
Published: over 3 years ago

10.1038/srep43364

Ethylene-induced transcriptional and hormonal responses at the onset of sugarcane ripening
Cited by: 34
Author(s): Camila Pinto da Cunha, Guilherme Garcia Roberto, Renato Vicentini, Carolina Gimiliani Lembke, Gláucia Mendes Souza, Rafael Vasconcelos Ribeiro, Eduardo Caruso Machado, Ana Maria Magalhães Andrade Lagôa, Marcelo Menossi
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2164-15-527

Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)
Cited by: 73
Author(s): Eli Meyer, Michael J. Aspinwall, David B. Lowry, Juan Diego Palacio-Mejía, Tierney L. Logan, Philip A. Fay, Thomas E. Juenger
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12870-015-0449-x

Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits
Cited by: 36
Author(s): Shiri Freilich, Shery Lev, Itay Gonda, Eli Reuveni, Vitaly Portnoy, Elad Oren, Marc Lohse, Navot Galpaz, Einat Bar, Galil Tzuri, Guy Wissotsky, Ayala Meir, Joseph Burger, Yaakov Tadmor, Arthur A. Schaffer, Zhangjun Fei, James J. Giovannoni, Efraim Lewinsohn, Nurit Katzir
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12870-019-2021-6

Exploring gene networks in two sunflower lines with contrasting leaf senescence phenotype using a system biology approach
Cited by: 9
Author(s): Sebastián Moschen, Johanna Marino, Salvador Nicosia, Janet Higgins, Saleh Alseekh, Francisco Horacio Astigueta, Sofía A. Bengoa Luoni, Máximo Rivarola, Alisdair R. Fernie, Nicolas Blanchet, Nicolas B. Langlade, Norma Paniego, Paula Fernández, Ruth Amelia Heinz
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-016-2593-6

Regulatory modules controlling early shade avoidance response in maize seedlings
Cited by: 41
Author(s): Hai Wang, Guangxia Wu, Binbin Zhao, Baobao Wang, Zhihong Lang, Zhang Chunyi, Haiyang Wang
Software Mentions: 2
Published: over 8 years ago

10.1186/s12870-021-02850-9

Reduced expression of a subunit gene of sucrose non-fermenting 1 related kinase, PpSnRK1βγ, confers flat fruit abortion in peach by regulating sugar and starch metabolism
Cited by: 1
Author(s): Jian Guo, Ke Cao, Jia‐Long Yao, Cecilia Deng, Yong Li, Guoqiang Zhu, Weichao Fang, Chang Wen Chen, Xinwei Wang, Jinlong Wu, Wen‐Wu Guo, Lirong Wang
Software Mentions: 2
Published: almost 4 years ago

Projects: cran: Mercator

Papers Mentioning Mercator 347